Investigating extended regulatory regions of genomic DNA sequences

Motivation: Despite the growing volume of data on primary nucleotide sequen ces, the regulatory regions remain a major puzzle with regard to their func tion. Numerous recognising programs considering a diversity of properties o f regulatory regions have been developed The system proposed here allows th e specific contextual, conformational and physico-chemical properties to be revealed based on analysis of extended DNA regions. Results: The Internet-accessible computer system RegScan, designed to analy se the extended regulatory regions of eukaryotic genes, has been developed The computer system comprises the following software: (i) programs for clas sification dividing a set of promoters into TATA-containing and TATA-less p romoters and promoters with and without CpG islands; (ii) programs for cons tructing (a) nucleotide frequency profiles, (b) sequence complexity profile s and (c) profiles of conformational and physio-chemical properties; (iii) the program for constructing the sets of degenerate oligonucleotide motifs of a specified length; and (iv) the program searching for and visualising r epeats in nucleotide sequences. The system has allowed us to demonstrate th e following characteristic patterns of vertebrate promoter regions: the TAT A box region is flanked by regions with all increased G+C content and incre ased bending stiffness, the TATA box content is asymmetric and promoter reg ions are saturated with both direct and inverted repeats. Availability: The computer system RegScan is available via the Internet at http://www.mgs.bionet.nsc.ru/Systems/ RegScan, http://www.cbil.upenn.edu/mg s/systems/regscan/ Contact: bob@bionet.nsc.ru.